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Nucleic Acids Research Advance Access originally published online on January 30, 2009
Nucleic Acids Research 2009 37(5):e36; doi:10.1093/nar/gkp034
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Nucleic Acids Research, 2009, Vol. 37, No. 5 e36
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Integrating sequence with FPC fingerprint maps

William Nelson and Carol Soderlund*

Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, AZ, USA

*To whom correspondence should be addressed. Tel: 520 626 9600; Fax: 520 626 4824; Email: cari{at}agcol.arizona.edu

Received June 26, 2008. Revised January 2, 2009. Accepted January 8, 2009.

Recent advances in both clone fingerprinting and draft sequencing technology have made it increasingly common for species to have a bacterial artificial clone (BAC) fingerprint map, BAC end sequences (BESs) and draft genomic sequence. The FPC (fingerprinted contigs) software package contains three modules that maximize the value of these resources. The BSS (blast some sequence) module provides a way to easily view the results of aligning draft sequence to the BESs, and integrates the results with the following two modules. The MTP (minimal tiling path) module uses sequence and fingerprints to determine a minimal tiling path of clones. The DSI (draft sequence integration) module aligns draft sequences to FPC contigs, displays them alongside the contigs and identifies potential discrepancies; the alignment can be based on either individual BES alignments to the draft, or on the locations of BESs that have been assembled into the draft. FPC also supports high-throughput fingerprint map generation as its time-intensive functions have been parallelized for Unix-based desktops or servers with multiple CPUs. Simulation results are provided for the MTP, DSI and parallelization. These features are in the FPC V9.3 software package, which is freely available.


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